Locus 4617

Sequence ID	3R_DroMel_CAF1
Location	12,142,145 – 12,142,275
Length	130
Max. P	0.998741

overview

Window 8

Location	12,142,145 – 12,142,246
Length	101
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-25.63
Consensus MFE	-22.70
Energy contribution	-22.90
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.89
SVM decision value	3.21
SVM RNA-class probability	0.998741
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12142145 101 - 27905053
CACUCUCAAGUGGCUCAUUGAGUUGCCUGCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUGGGCAUCUC------CAUCUAUCAGCUAUUUG
......(((((((((.((.(((.((((((....)......................((((((......)))))).))))).)))------.....)).))))))))) ( -24.20)
>DroSec_CAF1 48527 101 - 1
CACUCUCAAGUGGCUCAUUGAGUUGGCUUCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUCGGCAUCUC------CAUCUAUCAGCUAUUUG
......(((((((((...((((((((..................))))))))((..((((((......))))))..))......------........))))))))) ( -24.17)
>DroSim_CAF1 48841 101 - 1
CACUCUCAAGUGGCUCAUUGAGUUGGCUUCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUCGGCAUCUC------CAUCUAUCAGCUAUUUG
......(((((((((...((((((((..................))))))))((..((((((......))))))..))......------........))))))))) ( -24.17)
>DroEre_CAF1 48281 101 - 1
CACUCUCAAGUGGCUCAUUGAGUUGGCUUCUAGCCAUCCAUGUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUGGGCAUCUC------CAUCUAUCAGCUAUUUG
......(((((((((.((.((..((((.....))))...((((.((((..(((((.((.......)).)))))))))))))...------..)).)).))))))))) ( -27.50)
>DroYak_CAF1 60015 107 - 1
CACUCUCAAGUGGCUCAUUGAGUUGGCUUCUAGCCAUCCAUAUAGCAAUGCAUCUUGCAUCCACCGCCGGAUGUUGGGCAUCUCCAUCUCCAUCUAUCAGCUAUUUG
......(((((((((.((.((..((((.....))))........((...((((((.((.......)).))))))...)).............)).)).))))))))) ( -28.10)
>consensus
CACUCUCAAGUGGCUCAUUGAGUUGGCUUCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUGGGCAUCUC______CAUCUAUCAGCUAUUUG
......(((((((((.((.((..((((.....))))................((..((((((......))))))..))..............)).)).))))))))) (-22.70 = -22.90 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	12,142,170 – 12,142,275
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	94.06
Mean single sequence MFE	-30.35
Consensus MFE	-25.66
Energy contribution	-26.10
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.27
Structure conservation index	0.85
SVM decision value	0.03
SVM RNA-class probability	0.548396
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12142170 105 + 27905053
CAACAUCCGGCGGUGGAUGCAAGAUGAAUUGGUAUAUGGAUGGCUGGCAGGCAACUCAAUGAGCCACUUGAGAGUGGGACAAUAGAGAAAGCCCCCCCCACUCUA
...((((..(((.....)))..))))..............(((((.(.((....))...).)))))....((((((((..................)))))))). ( -28.47)
>DroSec_CAF1 48552 104 + 1
GAACAUCCGGCGGUGGAUGCAAGAUGAAUUGGUAUAUGGAUGGCUGGAAGCCAACUCAAUGAGCCACUUGAGAGUGGCACAAUAGAGAAAGCAC-CCCCACUCCA
........((.(((((.(((....................((((.....)))).(((..((.((((((....)))))).))...)))...))).-..))))))). ( -30.40)
>DroSim_CAF1 48866 104 + 1
GAACAUCCGGCGGUGGAUGCAAGAUGAAUUGGUAUAUGGAUGGCUGGAAGCCAACUCAAUGAGCCACUUGAGAGUGGCACAAUAGAGAAAGCAC-CCCCACUCCA
........((.(((((.(((....................((((.....)))).(((..((.((((((....)))))).))...)))...))).-..))))))). ( -30.40)
>DroEre_CAF1 48306 103 + 1
CAACAUCCGGCGGUGGAUGCAAGAUGAAUUGGUACAUGGAUGGCUAGAAGCCAACUCAAUGAGCCACUUGAGAGUGGCACAAUAGAGAAAGC-C-UCCCAAUCCA
...((((..(((.....)))..)))).(((((.....((.((((.....)))).(((..((.((((((....)))))).))...)))....)-)-..)))))... ( -29.70)
>DroYak_CAF1 60046 103 + 1
CAACAUCCGGCGGUGGAUGCAAGAUGCAUUGCUAUAUGGAUGGCUAGAAGCCAACUCAAUGAGCCACUUGAGAGUGGCACAAUAGAGAAAGC-C-UCCCACUCCA
........((.(((((((((.....)))).(((.......((((.....)))).(((..((.((((((....)))))).))...)))..)))-.-..))))))). ( -32.80)
>consensus
CAACAUCCGGCGGUGGAUGCAAGAUGAAUUGGUAUAUGGAUGGCUGGAAGCCAACUCAAUGAGCCACUUGAGAGUGGCACAAUAGAGAAAGC_C_CCCCACUCCA
...((((..(((.....)))..))))...(((....(((.((((.....)))).(((..((.((((((....)))))).))...)))..........)))..))) (-25.66 = -26.10 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	12,142,170 – 12,142,275
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	94.06
Mean single sequence MFE	-37.30
Consensus MFE	-30.00
Energy contribution	-30.12
Covariance contribution	0.12
Combinations/Pair	1.04
Mean z-score	-3.19
Structure conservation index	0.80
SVM decision value	2.62
SVM RNA-class probability	0.995799
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12142170 105 - 27905053
UAGAGUGGGGGGGGCUUUCUCUAUUGUCCCACUCUCAAGUGGCUCAUUGAGUUGCCUGCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUG
..(..(((((.((((...(((...((..(((((....)))))..))..)))..)))).))..)))..).................((((((......)))))).. ( -33.70)
>DroSec_CAF1 48552 104 - 1
UGGAGUGGGG-GUGCUUUCUCUAUUGUGCCACUCUCAAGUGGCUCAUUGAGUUGGCUUCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUC
((((.(((.(-(.(((..(((...((.((((((....)))))).))..)))..)))..))..)))))))................((((((......)))))).. ( -37.40)
>DroSim_CAF1 48866 104 - 1
UGGAGUGGGG-GUGCUUUCUCUAUUGUGCCACUCUCAAGUGGCUCAUUGAGUUGGCUUCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUC
((((.(((.(-(.(((..(((...((.((((((....)))))).))..)))..)))..))..)))))))................((((((......)))))).. ( -37.40)
>DroEre_CAF1 48306 103 - 1
UGGAUUGGGA-G-GCUUUCUCUAUUGUGCCACUCUCAAGUGGCUCAUUGAGUUGGCUUCUAGCCAUCCAUGUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUG
((((((((((-(-(((..(((...((.((((((....)))))).))..)))..))))))..((.......)).))))))))....((((((......)))))).. ( -39.30)
>DroYak_CAF1 60046 103 - 1
UGGAGUGGGA-G-GCUUUCUCUAUUGUGCCACUCUCAAGUGGCUCAUUGAGUUGGCUUCUAGCCAUCCAUAUAGCAAUGCAUCUUGCAUCCACCGCCGGAUGUUG
((((((.(((-(-(((..(((...((.((((((....)))))).))..)))..))))))).))..)))).........((((((.((.......)).)))))).. ( -38.70)
>consensus
UGGAGUGGGG_G_GCUUUCUCUAUUGUGCCACUCUCAAGUGGCUCAUUGAGUUGGCUUCCAGCCAUCCAUAUACCAAUUCAUCUUGCAUCCACCGCCGGAUGUUG
((((.(((.(...(((..(((...((.((((((....)))))).))..)))..)))...)..)))))))................((((((......)))))).. (-30.00 = -30.12 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:46 2006